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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ), 'gf_id' => 'HOM05D001277', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001277' ), 'data_identifier' => 'HOM05D001277', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001277', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '88' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12340' => 'bna', 'A03p52580' => 'bna', 'Aa31LG6G3030' => 'aar', 'Actinidia01875' => 'ach', 'Actinidia04985' => 'ach', 'Actinidia04986' => 'ach', 'Actinidia04987' => 'ach', 'Actinidia04988' => 'ach', 'Actinidia05642' => 'ach', 'Actinidia07314' => 'ach', 'Actinidia07315' => 'ach', 'Actinidia07316' => 'ach', 'Actinidia11023' => 'ach', 'Actinidia11024' => 'ach', 'Actinidia11081' => 'ach', 'Actinidia11082' => 'ach', 'Actinidia16554' => 'ach', 'Actinidia33058' => 'ach', 'Ah.02g110450' => 'amhyb', 'Ah.14g089470' => 'amhyb', 'Ah.14g089480' => 'amhyb', 'AL7G33180' => 'aly', 'Aqoxy3G01012' => 'aox', 'arahy.Tifrunner.gnm1.ann1.31ALDJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.92JXLG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AYVG4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B833GN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BQIR8X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CV46MP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CWTI60' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MB81X2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNAU2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QZ4ZPY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1IQ3S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VZ7M1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y49D7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YFEV2R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZXK4R3' => 'arhy', 'AT4G20970' => 'ath', 'ATR0737G008' => 'atr', 'Atru.chr11.2024' => 'acertr', 'Atru.chr3.2847' => 'acertr', 'Atru.chr3.2850' => 'acertr', 'Atru.chr6.2333' => 'acertr', 'Atru.chr6.2982' => 'acertr', 'Atru.chr9.2450' => 'acertr', 'AUR62008225' => 'cqu', 'AUR62008226' => 'cqu', 'AUR62014828' => 'cqu', 'AUR62014829' => 'cqu', 'AUR62017023' => 'cqu', 'AUR62030981' => 'cqu', 'BcaB03g11706' => 'bca', 'BcaC01g00725' => 'bca', 'BcaC09g51284' => 'bca', 'BcaC09g51289' => 'bca', 'BcaNung04715' => 'bca', 'BolC1t01430H' => 'bol', 'BolC3t20644H' => 'bol', 'BraA03t14332Z' => 'bra', 'BraA08t33516Z' => 'bra', 'C01p14830' => 'bna', 'C07p51020' => 'bna', 'CAN.G1164.47' => 'can', 'CAN.G1509.8' => 'can', 'CAN.G1600.2' => 'can', 'CAN.G578.14' => 'can', 'CAN.G578.9' => 'can', 'CAN.G781.19' => 'can', 'CAN.G781.21' => 'can', 'CANSAT35G1497' => 'cansat', 'CANSAT64G1763' => 'cansat', 'CANSAT80G1563' => 'cansat', 'CARHR227520' => 'chi', 'Carub.0007s2047' => 'cru', 'Cc00_g31280' => 'ccan', 'Cc02_g13460' => 'ccan', 'Cc04_g13690' => 'ccan', 'Cc04_g13700' => 'ccan', 'Cc05_g07290' => 'ccan', 'Cc05_g07300' => 'ccan', 'Cc05_g07310' => 'ccan', 'Cc05_g07320' => 'ccan', 'Cc11_g14670' => 'ccan', 'Cfa000483' => 'cfa', 'Cfa014626' => 'cfa', 'Cfa019101' => 'cfa', 'Cfa019102' => 'cfa', 'Ciclev10016466m.g' => 'ccl', 'Ciclev10016846m.g' => 'ccl', 'Ciclev10016938m.g' => 'ccl', 'Ciclev10017474m.g' => 'ccl', 'Ciclev10017617m.g' => 'ccl', 'Ciclev10018120m.g' => 'ccl', 'Ciclev10018141m.g' => 'ccl', 'Ciclev10022480m.g' => 'ccl', 'Ciclev10024201m.g' => 'ccl', 'CiPaw.03G178400' => 'cil', 'CiPaw.04G127400' => 'cil', 'CiPaw.09G060700' => 'cil', 'CiPaw.10G049700' => 'cil', 'CiPaw.11G027900' => 'cil', 'CiPaw.11G028000' => 'cil', 'CiPaw.11G028100' => 'cil', 'CiPaw.12G025400' => 'cil', 'CiPaw.12G025500' => 'cil', 'CiPaw.12G025600' => 'cil', 'ClCG01G013070' => 'cla', 'ClCG02G017710' => 'cla', 'ClCG05G023890' => 'cla', 'ClCG07G002820' => 'cla', 'COL.COLO4_07560' => 'col', 'COL.COLO4_10879' => 'col', 'COL.COLO4_24159' => 'col', 'COL.COLO4_31458' => 'col', 'COL.COLO4_36348' => 'col', 'COL.COLO4_36769' => 'col', 'COL.COLO4_36774' => 'col', 'Cpa.g.sc124.41' => 'cpa', 'Cpa.g.sc1938.2' => 'cpa', 'Cpa.g.sc27.35' => 'cpa', 'Cpa.g.sc69.31' => 'cpa', 'Cpa.g.sc69.33' => 'cpa', 'CsaV3_1G008410' => 'csa', 'CsaV3_1G012350' => 'csa', 'CsaV3_6G012850' => 'csa', 'CsaV3_7G004510' => 'csa', 'CSS0006604' => 'camsi', 'CSS0006867' => 'camsi', 'CSS0009069' => 'camsi', 'CSS0018561' => 'camsi', 'CSS0029869' => 'camsi', 'CSS0033336' => 'camsi', 'CSS0033518' => 'camsi', 'CSS0041963' => 'camsi', 'CSS0042783' => 'camsi', 'CSS0044106' => 'camsi', 'CSS0045340' => 'camsi', 'DCAR_004071' => 'dca', 'DCAR_010194' => 'dca', 'DCAR_021251' => 'dca', 'DCAR_022002' => 'dca', 'DCAR_024900' => 'dca', 'DCAR_024901' => 'dca', 'DCAR_026126' => 'dca', 'Dinv00852' => 'din', 'Dinv08385' => 'din', 'Dinv08386' => 'din', 'Dinv09151' => 'din', 'Dinv15296' => 'din', 'Dinv15297' => 'din', 'Dinv15299' => 'din', 'Dinv17320' => 'din', 'Dinv20667' => 'din', 'Dinv22070' => 'din', 'Dinv24853' => 'din', 'Dinv24854' => 'din', 'Dinv24856' => 'din', 'Dinv24857' => 'din', 'Dinv27918' => 'din', 'Dinv27986' => 'din', 'Dinv34968' => 'din', 'Dinv40569' => 'din', 'Duzib052G0158' => 'dzi', 'Duzib052G0658' => 'dzi', 'Duzib068G1427' => 'dzi', 'Duzib128G0068' => 'dzi', 'Duzib160G0013' => 'dzi', 'Duzib192G0366' => 'dzi', 'Duzib205G0114' => 'dzi', 'Duzib235G1150' => 'dzi', 'Duzib248G0806' => 'dzi', 'Duzib248G0856' => 'dzi', 'Duzib248G1354' => 'dzi', 'Duzib268G1467' => 'dzi', 'ECA233G3895' => 'eca', 'ECA234G0472' => 'eca', 'ECA246G0285' => 'eca', 'ECA247G0456' => 'eca', 'EL10Ac5g10766' => 'bvu', 'EL10Ac5g10767' => 'bvu', 'EL10Ac5g10768' => 'bvu', 'EL10Ac5g10769' => 'bvu', 'EL10Ac5g10771' => 'bvu', 'EL10Ac8g20389' => 'bvu', 'EL10Ac8g20390' => 'bvu', 'EL10Ac8g20391' => 'bvu', 'Eucgr.B00366' => 'egr', 'Eucgr.D00616' => 'egr', 'Eucgr.E03270' => 'egr', 'Eucgr.E03271' => 'egr', 'Eucgr.E03272' => 'egr', 'Eucgr.E03273' => 'egr', 'Eucgr.K01037' => 'egr', 'Eucgr.K01038' => 'egr', 'Eucgr.K01039' => 'egr', 'Eucgr.K02849' => 'egr', 'Eucgr.K02851' => 'egr', 'Eucgr.K02854' => 'egr', 'Eucgr.K02855' => 'egr', 'FAN04G0760' => 'fan', 'FAN05G0233' => 'fan', 'FAN08G2507' => 'fan', 'FAN09G2322' => 'fan', 'FAN11G1827' => 'fan', 'FAN13G2787' => 'fan', 'FAN16G0938' => 'fan', 'FAN18G1626' => 'fan', 'FAN18G4206' => 'fan', 'FAN21G1519' => 'fan', 'FAN25G3660' => 'fan', 'FvH4_3g09050' => 'fve', 'FvH4_5g05180' => 'fve', 'FvH4_6g26360' => 'fve', 'Glyma.04G182600' => 'gma', 'Glyma.05G036800' => 'gma', 'Glyma.06G291900' => 'gma', 'Glyma.07G197300' => 'gma', 'Glyma.12G114300' => 'gma', 'Glyma.12G205200' => 'gma', 'Glyma.13G178800' => 'gma', 'Glyma.13G238300' => 'gma', 'Glyma.13G296100' => 'gma', 'Glyma.15G075000' => 'gma', 'Glyma.17G090500' => 'gma', 'Glyma.U035800' => 'gma', 'Gohir.A03G096500' => 'ghi', 'Gohir.A04G103200' => 'ghi', 'Gohir.A04G135300' => 'ghi', 'Gohir.A05G299200' => 'ghi', 'Gohir.A06G128302' => 'ghi', 'Gohir.A10G026500' => 'ghi', 'Gohir.A12G138660' => 'ghi', 'Gohir.D02G117600' => 'ghi', 'Gohir.D04G142600' => 'ghi', 'Gohir.D04G178400' => 'ghi', 'Gohir.D05G164000' => 'ghi', 'Gohir.D06G132200' => 'ghi', 'Gohir.D10G027100' => 'ghi', 'Gohir.D12G142900' => 'ghi', 'Gorai.005G136000' => 'gra', 'Gorai.008G154300' => 'gra', 'Gorai.009G169200' => 'gra', 'Gorai.010G154100' => 'gra', 'Gorai.011G028400' => 'gra', 'Gorai.012G127900' => 'gra', 'Gorai.012G171500' => 'gra', 'GSVIVG01002788001' => 'vvi', 'GSVIVG01007117001' => 'vvi', 'GSVIVG01007772001' => 'vvi', 'GSVIVG01020561001' => 'vvi', 'HanXRQChr02g0037321' => 'han', 'HanXRQChr06g0171301' => 'han', 'HanXRQChr06g0171431' => 'han', 'HanXRQChr11g0327741' => 'han', 'HanXRQChr17g0541581' => 'han', 'HanXRQChr17g0560171' => 'han', 'Haze_06433' => 'cav', 'Haze_07498' => 'cav', 'Haze_07499' => 'cav', 'Haze_13181' => 'cav', 'Hma1.2p1_0002F.1_g001990' => 'hma', 'Hma1.2p1_0176F.1_g077575' => 'hma', 'Hma1.2p1_0176F.1_g077580' => 'hma', 'Hma1.2p1_0176F.1_g077590' => 'hma', 'Hma1.2p1_0176F.1_g077610' => 'hma', 'Hma1.2p1_0208F.1_g088180' => 'hma', 'Hma1.2p1_0536F.1_g174130' => 'hma', 'Hma1.2p1_1047F.1_g251590' => 'hma', 'Hma1.2p1_1734F.1_g299850' => 'hma', 'Hma1.2p1_2175F.1_g316090' => 'hma', 'HPP92_004859' => 'vpl', 'Hund23766' => 'sun', 'Lalb_Chr15g0089791' => 'lal', 'Lalb_Chr20g0121831' => 'lal', 'Lj3A1053G40' => 'lonja', 'Lj3g0021093' => 'lja', 'Lj4g0004622' => 'lja', 'Lj5g0009473' => 'lja', 'Lj6g0002586' => 'lja', 'Lsat_1_v5_gn_3_37760' => 'lsa', 'Lsat_1_v5_gn_4_52301' => 'lsa', 'Lsat_1_v5_gn_8_136380' => 'lsa', 'Lsat_1_v5_gn_8_157101' => 'lsa', 'Manes.06G103800' => 'mes', 'Manes.12G028900' => 'mes', 'Manes.12G088914' => 'mes', 'Manes.12G088952' => 'mes', 'Manes.13G145600' => 'mes', 'Manes.14G067000' => 'mes', 'Manes.16G028800' => 'mes', 'MBI07_g30190_MAGBIO' => 'mbi', 'MBI10_g11074_MAGBIO' => 'mbi', 'MBI16_g26458_MAGBIO' => 'mbi', 'MBI16_g26460_MAGBIO' => 'mbi', 'MBI16_g32805_MAGBIO' => 'mbi', 'MD05G1338200' => 'mdo', 'MD06G1176300' => 'mdo', 'MD06G1176600' => 'mdo', 'MD09G1233000' => 'mdo', 'MD14G1182700' => 'mdo', 'MD17G1237900' => 'mdo', 'MD17G1238500' => 'mdo', 'MD17G1238600' => 'mdo', 'Medtr2g013920' => 'mtr', 'Medtr2g090425' => 'mtr', 'Medtr2g090440' => 'mtr', 'Medtr2g090480' => 'mtr', 'Medtr2g090500' => 'mtr', 'Medtr2g090515' => 'mtr', 'Medtr4g078350' => 'mtr', 'Medtr7g055807' => 'mtr', 'MELO3C002257.2' => 'cme', 'MELO3C002608.2' => 'cme', 'MELO3C013627.2' => 'cme', 'MELO3C018728.2' => 'cme', 'Migut.M00292' => 'egut', 'Migut.M01136' => 'egut', 'MSTRG.6796' => 'ama', 'MSTRG.9675' => 'ama', 'Nitab4.5_0000852g0070' => 'nta', 'Nitab4.5_0000852g0080' => 'nta', 'Nitab4.5_0000908g0050' => 'nta', 'Nitab4.5_0001724g0100' => 'nta', 'Nitab4.5_0003857g0010' => 'nta', 'Nitab4.5_0006305g0020' => 'nta', 'Nitab4.5_0008267g0010' => 'nta', 'Nitab4.5_0011698g0010' => 'nta', 'Nitab4.5_0011698g0020' => 'nta', 'Nitab4.5_0015542g0010' => 'nta', 'Nitab4.5_0025245g0010' => 'nta', 'Nn1g04113' => 'nnu', 'Nn1g06509' => 'nnu', 'Nn3g16890' => 'nnu', 'Nn3g16897' => 'nnu', 'Nn3g16898' => 'nnu', 'Oeu005080.1' => 'oeu', 'Oeu017496.1' => 'oeu', 'Oeu017500.1' => 'oeu', 'Oeu017501.1' => 'oeu', 'Oeu024763.1' => 'oeu', 'Oeu030708.1' => 'oeu', 'Oeu064782.1' => 'oeu', 'Os01g0108400' => 'osa', 'Os01g0108600' => 'osa', 'Peaxi162Scf00008g00815' => 'pax', 'Peaxi162Scf00017g02837' => 'pax', 'Peaxi162Scf00059g01717' => 'pax', 'Peaxi162Scf00250g00016' => 'pax', 'Peaxi162Scf01057g00002' => 'pax', 'PGR004G0679' => 'pgr', 'PGR042G2152' => 'pgr', 'PGR044G0270' => 'pgr', 'PGR083G0118' => 'pgr', 'PGR142G0931' => 'pgr', 'PGSC0003DMG400007814' => 'stu', 'PGSC0003DMG400013148' => 'stu', 'PGSC0003DMG400024597' => 'stu', 'PGSC0003DMG400024598' => 'stu', 'PGSC0003DMG400029728' => 'stu', 'PGSC0003DMG400039921' => 'stu', 'Phvul.002G229100' => 'pvu', 'Phvul.003G199500' => 'pvu', 'Phvul.005G102700' => 'pvu', 'Phvul.005G102800' => 'pvu', 'Phvul.005G102900' => 'pvu', 'Phvul.006G184600' => 'pvu', 'Phvul.009G179600' => 'pvu', 'Phvul.011G119500' => 'pvu', 'Potri.004G044400' => 'ptr', 'Potri.011G053400' => 'ptr', 'Potri.012G079100' => 'ptr', 'Potri.013G129800' => 'ptr', 'Potri.015G074500' => 'ptr', 'Potri.019G034700' => 'ptr', 'Potri.019G099300' => 'ptr', 'Potri.019G099400' => 'ptr', 'Potri.019G099500' => 'ptr', 'Prupe.3G131500' => 'ppe', 'Prupe.4G048500' => 'ppe', 'Prupe.5G175200' => 'ppe', 'Prupe.5G175300' => 'ppe', 'Psat0s9061g0040' => 'psa', 'Psat1g204520' => 'psa', 'Psat5g272400' => 'psa', 'Psat5g272520' => 'psa', 'Psat5g272560' => 'psa', 'Psat5g272640' => 'psa', 'Psat5g272800' => 'psa', 'Psat7g167280' => 'psa', 'PSO135G0019' => 'pso', 'PSO135G0091' => 'pso', 'PSO339G4789' => 'pso', 'PSO384G1301' => 'pso', 'PSO384G1836' => 'pso', 'PSO384G4140' => 'pso', 'PSO478G2453' => 'pso', 'PSO478G3800' => 'pso', 'PSO675G4892' => 'pso', 'PSO724G0254' => 'pso', 'PSO732G0319' => 'pso', 'QL05p040966' => 'qlo', 'QL08p039190' => 'qlo', 'QL10p011975' => 'qlo', 'RcHm_v2.0_Chr2g0126861' => 'rch', 'RcHm_v2.0_Chr5g0008581' => 'rch', 'RcHm_v2.0_Chr5g0008601' => 'rch', 'RcHm_v2.0_Chr7g0193761' => 'rch', 'Rhsim02G0131400' => 'rsi', 'Rhsim06G0141200' => 'rsi', 'Rhsim08G0170900' => 'rsi', 'Rhsim12G0163800' => 'rsi', 'Sabra11G0037200' => 'sbr', 'Sabra12G0056700' => 'sbr', 'Sabra13G0107700' => 'sbr', 'Sabra15G0098400' => 'sbr', 'Sabra19G0110300' => 'sbr', 'SalBow2G0128' => 'sbo', 'SalBow2G2868' => 'sbo', 'SalBow7G0167' => 'sbo', 'SalBow7G1009' => 'sbo', 'SalBow8G2908' => 'sbo', 'SalBow8G4667' => 'sbo', 'Sc04g0001860' => 'sci', 'Sc05g0007630' => 'sci', 'Sc17g0006160' => 'sci', 'Sed0005239' => 'sed', 'Sed0008438' => 'sed', 'Sed0009274' => 'sed', 'Sed0012989' => 'sed', 'Sed0024653' => 'sed', 'SEGI_20630' => 'sgi', 'SGA_v2.0_scaffold22G09702' => 'sas', 'SGA_v2.0_scaffold7G04124' => 'sas', 'Solyc02g078130.3' => 'sly', 'Solyc03g114230.2' => 'sly', 'Solyc03g114233.1' => 'sly', 'Solyc03g114237.1' => 'sly', 'Solyc10g008243.1' => 'sly', 'Solyc10g008247.1' => 'sly', 'Solyc10g008260.2' => 'sly', 'Solyc10g008263.1' => 'sly', 'Solyc10g008270.3' => 'sly', 'Solyc12g010585.1' => 'sly', 'Solyc12g010595.1' => 'sly', 'Sopen02g022960' => 'spe', 'Sopen03g033330' => 'spe', 'Sopen10g004110' => 'spe', 'Sopen10g004130' => 'spe', 'Sopen12g005590' => 'spe', 'Sopen12g005610' => 'spe', 'Sp7g19040' => 'spa', 'TAR371G0133' => 'tar', 'TAR622G0406' => 'tar', 'TAR629G0294' => 'tar', 'TAR629G1074' => 'tar', 'TAR680G0001' => 'tar', 'TAR680G0004' => 'tar', 'THA.LOC104812267' => 'tha', 'THA.LOC104812938' => 'tha', 'Thecc.02G181300' => 'tca', 'Thecc.02G248700' => 'tca', 'Thecc.02G248800' => 'tca', 'Thecc.02G249300' => 'tca', 'Thecc.03G010300' => 'tca', 'Thecc.06G186100' => 'tca', 'Thecc.10G060700' => 'tca', 'Thecc.10G061000' => 'tca', 'Thecc.10G061400' => 'tca', 'Thhalv10026322m.g' => 'esa', 'TPR.G16512' => 'tpr', 'TPR.G6414' => 'tpr', 'TPR.G6429' => 'tpr', 'TWI36G0357' => 'twi', 'TWI36G0964' => 'twi', 'TWI36G1270' => 'twi', 'TWI36G1746' => 'twi', 'TWI38G2139' => 'twi', 'TWI59G0794' => 'twi', 'TWI63G1592' => 'twi', 'vmacro15915' => 'vma', 'vmacro16602' => 'vma', 'vmacro16603' => 'vma', 'VMungo0251G2181' => 'vmu', 'VMungo0540G1089' => 'vmu', 'VMungo1080G0239' => 'vmu', 'VMungo1080G0435' => 'vmu', 'VMungo1080G1159' => 'vmu', 'VMungo1127G0585' => 'vmu', 'VMungo1215G1091' => 'vmu', 'VMungo1309G3071' => 'vmu', 'Zm00001eb126610' => 'zma' ) $gf_id = 'HOM05D001277' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001277' ) $data_identifier = 'HOM05D001277' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 4, 'aar' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 5, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 1, 'cru' => (int) 1, 'ccan' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 9, 'cil' => (int) 10, 'cla' => (int) 4, 'col' => (int) 7, 'cpa' => (int) 5, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 18, 'dzi' => (int) 12, 'eca' => (int) 4, 'bvu' => (int) 8, 'egr' => (int) 13, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 10, 'vpl' => (int) 1, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mbi' => (int) 5, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 8, 'ptr' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 11, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'sly' => (int) 11, 'spe' => (int) 6, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 2, 'tca' => (int) 9, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 8, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb126610' $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